3A67

Crystal Structure of HyHEL-10 Fv mutant LN31D complexed with hen egg white lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Contribution of asparagine residues to the stabilization of a proteinaceous antigen-antibody complex, HyHEL-10-hen egg white lysozyme

Yokota, A.Tsumoto, K.Shiroishi, M.Nakanishi, T.Kondo, H.Kumagai, I.

(2010) J.Biol.Chem. 285: 7686-7696

  • DOI: 10.1074/jbc.M109.089623
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Many germ line antibodies have asparagine residues at specific sites to achieve specific antigen recognition. To study the role of asparagine residues in the stabilization of antigen-antibody complexes, we examined the interaction between hen egg whi ...

    Many germ line antibodies have asparagine residues at specific sites to achieve specific antigen recognition. To study the role of asparagine residues in the stabilization of antigen-antibody complexes, we examined the interaction between hen egg white lysozyme (HEL) and the corresponding HyHEL-10 variable domain fragment (Fv). We introduced Ala and Asp substitutions into the Fv side chains of L-Asn-31, L-Asn-32, and L-Asn-92, which interact directly with residues in HEL via hydrogen bonding in the wild-type Fv-HEL complex, and we investigated the interactions between these mutant antibodies and HEL. Isothermal titration calorimetric analysis showed that all the mutations decreased the negative enthalpy change and decreased the association constants of the interaction. Structural analyses showed that the effects of the mutations on the structure of the complex could be compensated for by conformational changes and/or by gains in other interactions. Consequently, the contribution of two hydrogen bonds was minor, and their abolition by mutation resulted in only a slight decrease in the affinity of the antibody for its antigen. By comparison, the other two hydrogen bonds buried at the interfacial area had large enthalpic advantage, despite entropic loss that was perhaps due to stiffening of the interface by the bonds, and were crucial to the strength of the interaction. Deletion of these strong hydrogen bonds could not be compensated for by other structural changes. Our results suggest that asparagine can provide the two functional groups for strong hydrogen bond formation, and their contribution to the antigen-antibody interaction can be attributed to their limited flexibility and accessibility at the complex interface.


    Organizational Affiliation

    Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 6-6-11, Sendai 980-8579, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme binding ig kappa chain V23-J2 region
L
107N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IG VH, anti-lysozyme
H
114N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
Y
129Gallus gallusGene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.189 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 56.581α = 90.00
b = 56.581β = 90.00
c = 234.429γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance